Areas of expertise

• Physical Organic Chemistry 030505
• Medical Biochemistry: Proteins And Peptides (Incl. Medical Proteomics) 110106
• Structural Chemistry And Spectroscopy 030606
• Medicinal And Biomolecular Chemistry 0304
• Organic Chemistry 0305
• Computer Software 0803
• Bioinformatics 060102

Biography

Researcher's projects

Past student projects

Publications

• Abdelkader, E, Qianzhu, H, Tan, Y et al. 2021, 'Genetic Encoding of N⁶-(((Trimethylsilyl)methoxy)carbonyl)- l -lysine for NMR Studies of Protein-Protein and Protein-Ligand Interactions', Journal of the American Chemical Society, vol. 143, no. 2, pp. 1133-1143.
• Koehler Leman, J, Weitzner, B, Lewis, S et al. 2020, 'Macromolecular modeling and design in Rosetta: recent methods and frameworks', Nature Methods: techniques for life scientists and chemists, vol. 17, pp. 665-680.
• Qianzhu, H, Welegedara, A, Williamson, H et al. 2020, 'Genetic Encoding of para-Pentafluorosulfanyl Phenylalanine: A Highly Hydrophobic and Strongly Electronegative Group for Stable Protein Interactions', Journal of the American Chemical Society, vol. 142, no. 41, pp. 17277-17281.
• Yardeni, E, Bahrenberg, T, Stein, R et al. 2019, 'Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels', Scientific Reports, vol. 9.
• Nitsche, C, Onagi, H, Quek, J et al 2019, 'Biocompatible Macrocyclization between Cysteine and 2-Cyanopyridine Generates Stable Peptide Inhibitors', Organic Letters, vol. 21, no. 12, pp. 4709-4712.
• Bahramzadeh, A, Huber, T & Otting, G 2019, 'Three-Dimensional Protein Structure Determination Using Pseudocontact Shifts of Backbone Amide Protons Generated by Double-Histidine Co2+-Binding Motifs at Multiple Sites', Biochemistry, vol. 58, no. 30, pp. 3243-3250.
• Welegedara, A, Adams, L, Huber, T et al 2018, 'Site-Specific Incorporation of Selenocysteine by Genetic Encoding as a Photocaged Unnatural Amino Acid', Bioconjugate Chemistry, vol. 29, no. 7, pp. 2257-2264.
• Bahramzadeh, A, Jiang, H, Huber, T et al 2018, 'Two Histidines in an αâ€?Helix: A Rigid Co2+â€?Binding Motif for PCS Measurements by NMR Spectroscopy', Angewandte Chemie International Edition, vol. 57, no. 21, pp. 6226-6229pp.
• Pilla, K, Otting, G & Huber, T 2017, '3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data', in Jonathan Keith (ed.), Methods in Molecular Biology - Bioinformatics: Structure, Function and Applications, Humana Press Inc., USA, pp. 3-21pp.
• Welegedara, A, Yang, Y, Lee, M et al 2017, 'Double-Arm Lanthanide Tags Deliver Narrow Gd3+-Gd3+ Distance Distributions in Double Electron-Electron Resonance (DEER) Measurements', Chemistry, A European Journal, vol. 23, no. 48, pp. 11694-11702.
• Nitsche, C, Mahawaththage Don, M, Becker, W et al 2017, 'Site-selective tagging of proteins by pnictogen-mediated self-assembly', Chemical Communications, vol. 53, no. 79, pp. 10894-10897pp.
• Pilla, K, Otting, G & Huber, T 2017, 'Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts', Structure, vol. 25, no. 3, pp. 559-568.
• Pan, B, Yang, F, Ye, Y et al 2016, '3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy', Chemical Communications, vol. 52, no. 67, pp. 10237-10240.
• Yang, Y, Huang, F, Huber, T et al 2016, 'Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis', Journal of Biomolecular NMR, vol. 64, no. 2, pp. 103-113.
• Pilla, K, Otting, G & Huber, T 2016, 'Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins', Journal of Molecular Biology, vol. 428, no. 2, pp. 522-532.
• Chen, J, Yang, Y, Zhang, L et al. 2016, 'Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy', Physical Chemistry Chemical Physics, vol. 18, no. 8, pp. 5850-5859.
• Chen, W, Nitsche, C, Pilla, K et al 2016, 'Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets', Journal of the American Chemical Society, vol. 138, no. 13, pp. 4539-4546.
• Porter, J, Boon, P, Murray, T et al 2015, 'Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search', ACS chemical biology, vol. 10, no. 2, pp. 611-621.
• Chen, W, Kuppan, K, Lee, M et al. 2015, 'O-tert-Butyltyrosine, an NMR Tag for High-Molecular-Weight Systems and Measurements of Submicromolar Ligand Binding Affinities', Journal of the American Chemical Society, vol. 137, no. 13, pp. 4581-4586.
• Pilla, K, Leman, J, Otting, G et al. 2015, 'Capturing Conformational States in Proteins Using Sparse Paramagnetic NMR Data', PLOS ONE (Public Library of Science), vol. 10, no. 5, pp. e0127053-e0127053.
• Zhao, Y, Soh, T, Chan, K et al 2015, 'Flexibility of NS5 methyltransferase-polymerase linker region is essential for dengue virus replication', Journal of Virology, vol. 89, no. 20, pp. 10717-10721.
• Shishmarev, D, Wang, Y, Mason, C et al. 2014, 'Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy', Nucleic Acids Research, vol. 42, no. 4, pp. 2750-2757.
• Skarshewski, A, Stanton-Cook, M, Huber, T et al 2014, 'uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation', BMC Bioinformatics, vol. 15, no. 36, pp. 1-6.
• Edwards, D, Huber, T, Hussain, S et al 2014, 'Determining the oligomeric structure of proteorhodopsin by Gd3+-based pulsed dipolar spectroscopy of multiple distances', Structure, vol. 22, no. 11, pp. 1677-1686.
• Milthorpe, J, Rendell, A P & Huber, T 2014, 'PGAS-FMM: Implementing a distributed fast multipole method using the X10 programming language', Concurrency and Computation: Practice and Experience, vol. 26, issue 3, pp. 712-727. doi:10.1002/cpe.3039
• Matalon, E, Huber, T, Hagelueken, G et al 2013, 'Gadolinium(III) spin labels for high-sensitivity distance measurements in transmembrane helices', Angewandte Chemie International Edition, vol. 52, no. 45, pp. 11831-11834.
• Loh, C, Ozawa, K, Tuck, K et al 2013, 'Lanthanide tags for site-specific ligation to an unnatural amino acid and generation of pseudocontact shifts in proteins', Bioconjugate Chemistry, vol. 24, no. 2, pp. 260-268.
• Kaminker, I, Tkach, I, Manukovsky, N et al 2013, 'W-band orientation selective DEER measurements on a Gd³⁺/nitroxide mixed-labeled protein dimer with a dual mode cavity', Journal of Magnetic Resonance, vol. 227, pp. 66-71.
• Jergic, S, Horan, N, Elshenawy, M et al 2013, 'A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode', The EMBO Journal, vol. 32, no. 9, pp. 1322-1333.
• Li, J, Pilla, K.B, Li, Q et al 2013, 'Magic angle spinning NMR structure determination of proteins from pseudocontact shifts', Journal of the American Chemical Society, vol. 135, no. 22, pp. 8294-8303.
• Ozawa, K, Horan, N, Robinson, A et al 2013, 'Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits alpha, epsilon, theta and beta reveals a highly flexible arrangement of the proofreading domain', Nucleic Acids Research, vol. 41, no. 10, pp. 5354-5367.
• Yagi, H, Pilla, K, T, Maleckis, A et al 2013, 'Three-dimensional protein fold determination from backbone amide pseudocontact shifts generated by lanthanide tags at multiple sites', Structure, vol. 21, no. 6, pp. 883-890.
• Banerjee, D, Yagi, H, Huber, T et al 2012, 'Nanometer-range distance measurement in a protein using Mn²⁺ tags', Journal of Physical Chemistry Letters, vol. 3, no. 2, pp. 157-160.
• Loscha, K, Herlt, A, Qi, R et al 2012, 'Multiple-site labeling of proteins with unnatural amino acids', Angewandte Chemie International Edition, vol. 51, no. 9, pp. 2243-2246.
• Schmitz, C, Vernon, R, Otting, G et al 2012, 'Protein structure determination from pseudocontact shifts using ROSETTA', Journal of Molecular Biology, vol. 416, no. 5, pp. 668-677.
• Kaminker, I, Yagi, H, Huber, T et al 2012, 'Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd³⁺ spin labels', Physical Chemistry Chemical Physics, vol. 14, no. 13, pp. 4355-4358.
• Ding, T, Middelberg, A, Falconer, R et al 2012, 'Far-infrared spectroscopy analysis of linear and cyclic peptides, and lysozyme', Vibrational Spectroscopy, vol. 61, pp. 144-150.
• Graham, B, Loh, C, Swarbrick, J et al 2011, 'DOTA-amide lanthanide tag for reliable generation of pseudocontact shifts in protein NMR spectra', Bioconjugate Chemistry, vol. 22, no. 10, pp. 2118-2125.
• Ding, T, Huber, T, Middelberg, A et al 2011, 'Characterization of low-frequency modes in aqueous peptides using far-infrared spectroscopy and molecular dynamics simulation', Journal of Physical Chemistry A, vol. 115, no. 42, pp. 11559-11565.
• Jia, X, Maleckis, A, Huber, T et al 2011, '4,4 '-Dithiobisdipicolinic Acid: A Small and Convenient Lanthanide Binding Tag for Protein NMR Spectroscopy', Chemistry, A European Journal, vol. 17, no. 24, pp. 6830-6836.
• Swarbrick, J, Ung, P, Su, X et al. 2011, 'Engineering of a bis-chelator motif into a protein α-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy', Chemical Communications, vol. 47, no. 26, pp. 7368-7370.
• Yagi, H, Banerjee, D, Graham, B et al 2011, 'Gadolinium tagging for high-precision measurements of 6 nm distances in protein assemblies by EPR', Journal of the American Chemical Society, vol. 133, no. 27, pp. 10418-10421.
• Jia, X, Yagi, H, Su, X et al. 2011, 'Engineering [Ln(DPA)₃]^3- binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions', Journal of Biomolecular NMR, vol. 50, no. 4, pp. 411-420.
• de la Cruz, L, Nguyen, T, Ozawa, K et al 2011, 'Binding of low molecular weight inhibitors promotes large conformational changes in the dengue virus NS2B-NS3 protease: fold analysis by pseudocontact shifts', Journal of the American Chemical Society, vol. 133, no. 47, pp. 19205-19215.
• Nguyen T. H. D.; Ozawa K.; Stanton-Cook M.; Barrow R.; Huber T.; Otting G.; 2011, Generation of pseudocontact shifts in protein NMR spectra with a genetically encoded cobalt(II)-binding amino acid, Angewandte Chemie International Edition, 50, 692-694.
• Ding, T, Li, R, Zeitler, J et al 2010, 'Terahertz and far infrared spectroscopy of alanine-rich peptides having variable ellipticity', Optics Express, vol. 18, no. 26, pp. 27431-27444.
• Man, B, Su, X, Liang, H et al. 2010, '3-Mercapto-2,6-Pyridinedicarboxylic Acid: A Small Lanthanide-Binding Tag for Protein Studies by NMR Spectroscopy', Chemistry, A European Journal, vol. 16, no. 12, pp. 3827-3832.
• Yagi, H, Loscha, K, Su, X et al. 2010, 'Tunable paramagnetic relaxation enhancements by [Gd(DPA)₃]^3- for protein structure analysis', Journal of Biomolecular NMR, vol. 47, no. 2, pp. 143-153.
• Mouradov, D, Kobe, B, Dixon, N et al 2010, 'Hybrid methods for protein structure prediction', in H. Rangwala and G. Karypis (ed.), Introduction to Protein Structure Prediction, John Wiley & Sons Inc, Hoboken, NJ, pp. 265-277.
• Li, R, Ding, T, Huber, T et al 2009, 'Terahertz Time-Domain Spectroscopy of Peptides in Solution', International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz 2009), Institute of Electrical and Electronics Engineers (IEEE Inc), Korea, pp. 1-2.
• Kobe, B, Guncar, G, Buchholz, R et al 2009, 'The Many Faces of Platelet Glycoprotein Ibα - Thrombin Interaction', Current Protein and Peptide Science, vol. 10, no. 6, pp. 551-558.
• Li, S, Mouradov, D, King, G et al 2009, 'Study of protein three-dimensional structure and dynamics using peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) and chemical cross-linking with mass spectrometry to constrain molecular modeling', in Gu J, Bourne P (ed.), Structural Bioinformatics (2nd ed), Wiley-Blackwell, United States, pp. 171-206.
• Robin, G, Cowieson, N, Guncar, G et al 2008, 'A General Target Selection Method for Crystallographic Proteomics', in Kobe B, Guss M, Huber T (ed.), Structural Proteomics: High Throughput Methods, Humana Press Inc., Totowa, NJ, USA, pp. 27-37.
• Mouradov, D, King, G, Ross, I et al 2008, 'Protein Structure Determination Using a Combination of Cross-Linking, Mass Spectrometry, and Molecular Modeling', in Kobe B, Guss M, Huber T (ed.), Structural Proteomics: High Throughput Methods, Humana Press Inc., Totowa, NJ, USA, pp. 459-477.
• Kobe, B, Guss, J & Huber, T, eds, 2008, Structural Proteomics, Humana Press Inc., Totowa, NJ, USA.
• Meng, W, Forwood, J, Guncar, G et al 2008, 'Overview of the Pipeline for Structural and Functional Characterization of Macrophage Proteins at the University of Queensland', in Kobe B, Guss M, Huber T (ed.), Structural Proteomics: High Throughput Methods, Humana Press Inc., Totowa, NJ, USA, pp. 577-589.
• Su, X, McAndrew, K, Huber, T et al. 2008, 'Lanthanide-Binding Peptides for NMR Measurements of Residual Dipolar Couplings and Paramagnetic Effects from Multiple Angles', Journal of the American Chemical Society, vol. 130, no. 5, pp. 1681-1687.
• Saunders, N, Brinkworth, R, Huber, T et al 2008, 'Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites', BMC Bioinformatics, vol. 9, pp. 245:1-11.
• Su, X, Man, B, Beeren, S et al. 2008, 'A Dipicolinic Acid Tag for Rigid Lanthanide Tagging of Proteins and Paramagnetic NMR Spectroscopy', Journal of the American Chemical Society, vol. 130, no. 32, pp. 10486-10487.
• King, G, Jones, A, Kobe, B et al 2008, 'Identification of Disulfide-Containing Chemical Cross-Links in Proteins Using MALDI-TOF/TOF-Mass Spectrometry', Analytical Chemistry, vol. 80, no. 13, pp. 5036-5043.
• Cowieson, N, King, G, Cookson, D et al 2008, 'Cortactin Adopts a Globular Conformation and Bundles Actin into Sheets', Journal of Biological Chemistry, vol. 283, no. 23, pp. 16187-16193.
• Song, J, Yuan, Z, Tan, H et al 2008, 'Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure', Bioinformatics, vol. 23, no. 23, pp. 3147-3154.
• Schmitz, C, Stanton-Cook, M, Su, X et al. 2008, 'Numbat: an iteractive sotware tool for fitting Δ_χ-tensors to molecular coordinates using pseudocontact shifts', Journal of Biomolecular NMR, vol. 41, no. 3, pp. 179-189.
• Kobe, B, Guncar, G, Buchholz, R et al 2008, 'Crystallography and protein-protein interactions: biological interfaces and crystal contacts', Biochemical Society Transactions, vol. 36, no. 6, pp. 1438-1441.
• Hadler, K, Huber, T, Cassady, A et al 2008, 'Identification of a non-purple tartrate-resistant acid phosphatase: an evolutionary link to Ser/Thr protein phosphatases?', BMC Research Notes, vol. 1, no. 78, pp. 1-8.
• Forwood, J, Thakur, A, Guncar, G et al 2007, 'Structural basis for recruitment of tandem hotdog domains in acyl-CoA thioesterase 7 and its role in inflammation', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 25, pp. 10382-10387.
• Flanagan, J & Huber, T 2007, 'Structural Evolution of the ABC transporter Subfamily B', Evolutionary Bioinformatics, vol. 3, pp. 309-316.
• John, M, Schmitz, C, Park, A et al. 2007, 'Sequence-Specific and Stereospecific Assignment of Methyl Groups Using Paramagnetic Lanthanides', Journal of the American Chemical Society, vol. 129, no. 44, pp. 13749-13757.
• Su, X, Huber, T, Dixon, N et al. 2006, 'Site-Specific Labelling of Proteins with a Rigid Lanthanide-Binding Tag', ChemBioChem, vol. 7, no. 10, pp. 1599-1604.
• Mouradov, D, Craven, A, Forwood, J et al 2006, 'Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking', Protein Engineering Design and Selection, vol. 19, no. 1, pp. 9-16.
• Schmitz, C, John, M, Park, A et al. 2006, 'Efficient χ-tensor determination and NH assignment of paramagnetic proteins', Journal of Biomolecular NMR, vol. 35, no. 2, pp. 79-87.
• DeSantis, T, Hugenholtz, P, Larsen, N et al 2006, 'Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB', Applied and Environmental Microbiology, vol. 72, no. 7, pp. 5069-5072.
• Song, J, Burrage, K, Yuan, Z et al 2006, 'Perdiction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information', BMC Bioinformatics, vol. 7, no. 124, pp. 1-13.
• Puri, M, Robin, G, Cowieson, N et al 2006, 'Focusing in on structural genomics: The University of Queensland structural biology pipeline', Biomolecular Engineering (till 2008), vol. 23, no. 6, pp. 281-289.
• Aagaard, A, Listwan, P, Cowieson, N et al 2005, 'An Inflammatory Role for the Mammalian Carboxypeptidase Inhibitor Latexin: Relationship to Cystatins and the Tumour Suppressor TIG1', Structure, vol. 13, no. 2, pp. 309-317.
• Cowieson, N, Listwan, P, Kurz, M et al 2005, 'Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system', Journal of Structural and Functional Genomics, vol. 6, no. 1, pp. 13-20.
• Ozawa, K, Headlam, M, Mouradov, D et al. 2005, 'Translational incorporation of _L-3,4-dihydroxyphenylalanine into proteins', The FEBS Journal, vol. 272, no. 12, pp. 3162-3171.
• Potapov, A, Yagi, H, Huber, T et al 2010, 'Nanometer-Scale Distance Measurements in Proteins Using Gd³⁺ Spin Labeling', Journal of the American Chemical Society, vol. 132, no. 26, pp. 9040-9048.
• Huber, T & Torda, A 2002, 'Protein structure prediction by threading: Force field philosophy, approaches to alignment.', in Igor F. Tsigelny (ed.), Protein Structure Prediction: Bioinformatic Approach, International University Line, La Jolla, California, USA, pp. 263-296.
• Xu, Y, Carr, P, Huber, T et al. 2001, 'The structure of the P_II-ATP complex', European Journal of Biochemistry, vol. 268, no. 7, pp. 2028-2037.
• Reith, D, Huber, T, Mueller-Plathe, F et al. 2001, 'Free energy approximations in simple lattice proteins', Journal of Chemical Physics, vol. 114, no. 11, pp. 4998-5005.
• Abraham, M, Procter, J, Huber, T et al. 2001, 'Protein folding force fields: Optimisation and optimism', Biomedical Research in 2001, ed. Brian Lithgow and Irena Cosic, Monash University, Clayton, Victoria, pp. 111-114.
• Rendell, A, Bliznyuk, A, Huber, T et al 2000, 'Computational chemistry on Fujitsu vector-parallel processors: Development and performance of applications software', Parallel Computing, vol. 26, pp. 887-911.
• Huber, T & Torda, A 1999, 'Protein sequence threading, the alignment problem and a two step strategy', Journal of Computational Chemistry, vol. 20, pp. 1455-1467.
• Ayers, D, Huber, T & Torda, A 1999, 'Protein fold recognition force fields: unusual construction strategies', Proteins: Structure Function and Genetics, vol. 36, pp. 454-461.
• Scott, W, Hunenberger, P, Tironi, I et al 1999, 'The GROMOS biomolecular simulation program package', Journal of Computational Chemistry, vol. 103, pp. 3596-3607.
• Huber, T, Russell, A, Ayers, D et al 1999, 'Sausage: protein threading with flexible force fields', Bioinformatics, vol. 15, pp. 1064-1065.

Projects and Grants

Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.

• Enhanced high-field nuclear magnetic resonance spectroscopy (Secondary Investigator)
• Methods for Protein Structure Analysis by Electron Paramagnetic Resonance (Primary Investigator)
• New methods for drug discovery by NMR spectroscopy (Primary Investigator)
• Ultrafast magic angle spinning solid-state NMR capability (Secondary Investigator)
• Decrypting the Excitation Contraction coupling machinery in skeletal muscle (Secondary Investigator)
• New methods for protein design (Secondary Investigator)
• Tags and algorithms for studies of protein structures and interactions (Primary Investigator)
• 3D structure determination of biomolecular assemblies from sparse data of different length scales (Primary Investigator)
• Mapping protein contacts and conformational changes in macromolecular assemblies (Secondary Investigator)
• 3D Structure determination of biomacromolecular assemblies from sparse data (Primary Investigator)
• New fragment-based drug design technology by NMR spectroscopy (Secondary Investigator)

Related websites

• http://comp-bio.anu.edu.au/
  

  The biomolecular modelling & computational biology group website

• http://comp-bio.anu.edu.au/huber/Publications.html
  

  full list of publications